… b, UShER evaluations of the parsimony score for placing the sample S5 (blue) at each
possible position (Methods) of our example phylogeny (shown in a). We considered the branch …

… Specifically, we discover that the root of the B.1.355 lineage might have resulted from a
recombination event between nodes belonging to the B.1.595 and B.1.371 lineages (Fig. 3 and …

… Panel B is zoomed in on this subtree and its sister clade; at this scale, we can read individual
sample names and observe that this specific strain has been actively spreading in the …

… When multiple branches in T’ match the branch b in T with the same best split distance, we
report all best-matching branches (Methods). Additionally, we confirmed that our statistic is a …

… (B) Introners in Symbiodinium microadriaticum show clear evidence of 4 bp TSDs (shown
in green) and TIRs (underlined), consistent with many known DNA transposons, carry their 3′ …

… Specifically, we discover that the root of B.1.355 lineage might have resulted from a
recombination event between nodes belonging to the B.1.595 and B.1.371 lineages (Fig 3, Table S3)…

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and
they are among the most highly conserved and frequently transcribed genes in all living …

… The long-established nucleotide conservations, or semi-conservations, imposed on tRNA
sequences appear primarily in the loops and the portions of the A- and B-boxes in the D- and T…

… (B) An example of how matOptimize estimates the parsimony score improvement achievable
from a single SPR move using a small number of steps without redoing the entire Fitch …

… Below, wherever possible, we give the script name and line number responsible for a
computation, denoted as h e a d e r : l i n e _ n u m b e r . All code is in the s r c / directory within the …